John L. Markley

Publication Activity (10 Years)

Years Active: 2007-2021
Publications (10 Years): 7

Top Topics

Protein Structure

Top Venues

J. Biomed. Semant.

Database J. Biol. Databases Curation

Publications

Kumaran Baskaran, Jonathan R. Wedell, Eldon L. Ulrich, Jeffery C. Hoch, John L. Markley
PyBMRB: Data visualization tool for BioMagResBank. SciPy (2021)
Hongzhao Shao, Stephen Boulton, Cristina Olivieri, Hebatallah Mohamed, Madoka Akimoto, Manu Veliparambil Subrahmanian, Gianluigi Veglia, John L. Markley, Giuseppe Melacini, Woonghee Lee
CHESPA/CHESCA-SPARKY: automated NMR data analysis plugins for SPARKY to map protein allostery. Bioinform. 37 (8) (2021)
Daniel K. Weber, Songlin Wang, John L. Markley, Gianluigi Veglia, Woonghee Lee
PISA-SPARKY: an interactive SPARKY plugin to analyze oriented solid-state NMR spectra of helical membrane proteins. Bioinform. 36 (9) (2020)
John L. Markley, Hesam Dashti, Jonathan R. Wedell, William M. Westler, Eldon L. Ulrich, Hamid R. Eghbalnia
Approach to Improving the Quality of Open Data in the Universe of Small Molecules. BIS (Workshops) (2019)
Woonghee Lee, John L. Markley
PINE-SPARKY.2 for automated NMR-based protein structure research. Bioinform. 34 (9) (2018)
Jasmine Young, John D. Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M. Berrisford, Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand P. Gore, Vladimir Guranovic, Pieter M. S. Hendrickx, Brian P. Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica Sekharan, Chenghua Shao, Oliver S. Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. Database J. Biol. Databases Curation 2018 (2018)
Masashi Yokochi, Naohiro Kobayashi, Eldon L. Ulrich, Akira R. Kinjo, Takeshi Iwata, Yannis E. Ioannidis, Miron Livny, John L. Markley, Haruki Nakamura, Chojiro Kojima, Toshimichi Fujiwara
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. J. Biomed. Semant. 7 (2016)
Woonghee Lee, Marco Tonelli, John L. Markley
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy. Bioinform. 31 (8) (2015)
Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
The Protein Data Bank archive as an open data resource. J. Comput. Aided Mol. Des. 28 (10) (2014)
Woonghee Lee, Arash Bahrami, John L. Markley
ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy. Bioinform. 29 (4) (2013)
Jurgen F. Doreleijers, Wim F. Vranken, Christopher F. Schulte, John L. Markley, Eldon L. Ulrich, Gert Vriend, Geerten W. Vuister
NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB. Nucleic Acids Res. 40 (Database-Issue) (2012)
Woonghee Lee, John L. Markley
PACSY database, a relational database management system for Protein structure and nuclear Magnetic Resonance chemical shift analysis. BIBM Workshops (2012)
Woonghee Lee, Jin Hae Kim, William M. Westler, John L. Markley
PONDEROSA, an automated 3D-NOESY peak picking program, enables automated protein structure determination. Bioinform. 27 (12) (2011)
Woonghee Lee, William M. Westler, Arash Bahrami, Hamid Eghbalnia, John L. Markley
PINE-SPARKY: graphical interface for evaluating automated probabilistic peak assignments in protein NMR spectroscopy. Bioinform. 25 (16) (2009)
Arash Bahrami, Amir H. Assadi, John L. Markley, Hamid Eghbalnia
Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy. PLoS Comput. Biol. 5 (3) (2009)
Eldon L. Ulrich, Hideo Akutsu, Jurgen F. Doreleijers, Yoko Harano, Yannis E. Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller, Eiichi Nakatani, Christopher F. Schulte, David E. Tolmie, R. Kent Wenger, Hongyang Yao, John L. Markley
BioMagResBank. Nucleic Acids Res. 36 (Database-Issue) (2008)
Kim Henrick, Zukang Feng, Wolfgang Bluhm, Dimitris Dimitropoulos, Jurgen F. Doreleijers, Shuchismita Dutta, Judith L. Flippen-Anderson, John M. C. Ionides, Chisa Kamada, Eugene Krissinel, Catherine L. Lawson, John L. Markley, Haruki Nakamura, Richard H. Newman, Yukiko Shimizu, Jawahar Swaminathan, Sameer Velankar, Jeramia Ory, Eldon L. Ulrich, Wim F. Vranken, John D. Westbrook, Reiko Yamashita, Huanwang Yang, Jasmine Young, Muhammed Yousufuddin, Helen M. Berman
Remediation of the protein data bank archive. Nucleic Acids Res. 36 (Database-Issue) (2008)
Helen M. Berman, Kim Henrick, Haruki Nakamura, John L. Markley
The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35 (Database-Issue) (2007)
John L. Markley, Mark E. Anderson, Qiu Cui, Hamid Eghbalnia, Ian A. Lewis, Adrian D. Hegeman, Jing Li, Christopher F. Schulte, Michael R. Sussman, William M. Westler, Eldon L. Ulrich, Zsolt Zolnai
New Bioinformatics Resources For Metabolomics. Pacific Symposium on Biocomputing (2007)